Make smooth texture transition animation in BGE
I don't know whether you can fade between two materials, but you could easily set up a mix shader within a single material and animate the factor with keyframes.  So the single material would contain shader setups for your day sky and your night sky, and the mix shader would switch between the two.  It is possible to mix between background shaders FYI (although since you say you have a "skydome" perhaps you are talking about mesh materials, not background materials . . . it's the same principle either way).